In-silico derivation of microsatellite markers for fragrance in rice

An important quality trait in rice breeding is the production of basmati- and jasmine-style fragrance in cooked rice. This trait is controlled by a number of chemical constituents, however, it has been established that in most varieties a single recessive gene controls the most important chemical compound 2-acetyl-l-pyrroline (AP). Traditional methods of fragrance detection are through sensory or chemical means, however, each of these have their disadvantages. Microsatellite or simple sequence repeats (SSRs) have the ability to overcome the disadvantages. Using both the publicly available and restricted access sequence information of the Monsanto rice sequence databases, we have identified an (AT)40 repeat that easily distinguishes fragrant and non-fragrant alleles of the fgr gene. Using a mapping population of 50 F2 individuals, the polymorphic marker (PIC = 0.9) was genotyped and two recombinants identified, placing the marker at a maximum of 4 cM from the fgr gene. This study demonstrates that analysis of the rice genome sequence is an effective option for identification of markers for use in rice improvement.